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- PDB-3pmm: The crystal structure of a possible member of GH105 family from K... -

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Basic information

Entry
Database: PDB / ID: 3pmm
TitleThe crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
ComponentsPutative cytoplasmic protein
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / alpha/alpha toroid / cytoplasmic
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / IMIDAZOLE / Cytoplasmic protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.899 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Authors: Tan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 8, 2012Group: Other
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,32310
Polymers44,8851
Non-polymers4379
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.085, 143.085, 129.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein Putative cytoplasmic protein / GLYCOSYL HYDROLASE


Mass: 44885.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_23540, KPN_02389 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A6TB44
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole:HCl, 2.5M Sodium Chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→45.3 Å / Num. all: 52988 / Num. obs: 52988 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 29.41 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 45.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 12 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2621 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.899→45.247 Å / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 2646 5.09 %random
Rwork0.1557 ---
all0.1565 51937 --
obs0.1565 51937 97.83 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.309 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.452 Å20 Å2-0 Å2
2--0.452 Å20 Å2
3----0.904 Å2
Refinement stepCycle: LAST / Resolution: 1.899→45.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 29 341 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073248
X-RAY DIFFRACTIONf_angle_d0.9444400
X-RAY DIFFRACTIONf_dihedral_angle_d14.6611178
X-RAY DIFFRACTIONf_chiral_restr0.068458
X-RAY DIFFRACTIONf_plane_restr0.004569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8985-1.96640.24742440.214546X-RAY DIFFRACTION91
1.9664-2.04510.21642670.17444723X-RAY DIFFRACTION95
2.0451-2.13820.18012540.14784814X-RAY DIFFRACTION97
2.1382-2.25090.17042840.14344872X-RAY DIFFRACTION98
2.2509-2.3920.18272650.14784951X-RAY DIFFRACTION99
2.392-2.57660.17362470.1574996X-RAY DIFFRACTION99
2.5766-2.83590.18182740.16955005X-RAY DIFFRACTION100
2.8359-3.24610.19182610.17635062X-RAY DIFFRACTION100
3.2461-4.08940.15352870.14915069X-RAY DIFFRACTION100
4.0894-45.26030.15272630.14265253X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 74.1959 Å / Origin y: 39.2468 Å / Origin z: 42.9306 Å
111213212223313233
T0.2411 Å20.0031 Å2-0.0434 Å2-0.1488 Å2-0.084 Å2--0.1974 Å2
L0.6735 °20.1514 °2-0.1423 °2-0.379 °2-0.0151 °2--0.3986 °2
S-0.0024 Å °0.1285 Å °-0.1832 Å °-0.0847 Å °0.0435 Å °-0.0225 Å °0.1977 Å °-0.0189 Å °-0.0334 Å °
Refinement TLS groupSelection details: chain A

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